Javier Alberola was involved in a skirmish with the on-loan Atletico Madrid striker during the La Liga victory over Eibar.
As a result, Morata was left incensed after the official made contact with his neck in the closing stages.
At the full-time whistle, the Spain international attempted to confront the 27-year-old but was held back by teammates.
Despite Alberola insisting the contact was innocent, the Spanish FA decided to axe him from selection for the next two rounds of matches in the top flight.
After the match on Sunday, Atletico manager Diego Simeone leapt to the defence of Morata.
He said: “Morata was not happy. In fact, he was annoyed.
“That action reminded me when I was banned for four games when I did something similar to the fourth official.”
Atleti team-mate Koke added: “I had never seen a referee do something like that.
“He (Morata) felt a clip around the back of the neck and got annoyed at the referee. He is only human.